There are only 2 options to a user when they plan:
a) if you want to start your EM from new repository then you should do fresh install of EM
b) if you want to retain your history and everything in repository , then you should upgarde your EM from existing verstion to EM 12c

What you are asking is combination of above two options. It is not possible to pick and choose data from the EM repository to delete. EM repository is SYSMAN schema and it stores everything related to EM in variuos table, we donnt expose where what information goes in repository .. .. all these table have dependencies on each other. You cannt pick and choose to remove any thing.

If you are looking to some information to maintain an existing repository or EM then yes we have some infomration on that, in our guide